tbuckley/cabot-search huggingface dataset:
Abstract 2041: Research strategies for rare germline variants and cancer study
Authors: Seokhyeon Kim, Youngil Koh, Sung-Soo Yoon
Journal: Cancer Research (2023)

Abstract Exploration of rare germline variants in cancer is the fields of ongoing research. So, we would like to suggest several considerations for the rare pathogenic germline variants studies. We confirmed the pathogenicity of each variant using ClinVar (https://www.ncbi.nlm.nih.gov/clinvar). In addition, we utilized in silico prediction tools such as Polyphen and SIFT. Even for the same variant, the report of the variant may vary depending on the database used. We conducted rare germline variants screening using ICGC (International Cancer Genome Consortium) PCAWG (Pan-Cancer Analysis of Whole Genomes) data. we filtered allele frequencies using the gnomAD (v2.1.1) exome database. We utilized several ClinVar versions to check the clinical significance of germline variants. Next, we have investigated some in silico tools that predict ClinVar pathogenic and benign variants well. We observed inconsistent variant reports across versions of ClinVar. Although the information on variants may change over time, there have been inconsistent changes in the clinical significance of variants reported as P (Pathogenic) or LP (Likely pathogenic). The clinical significance of the variants reported in the previous version was P or LP, but those in the updated version were changed to “Conflicting interpretations of pathogenicity”. It was confirmed that the variant report changes when at least one “Uncertain Significance” review is added. Among various prediction tools, we found that the predictive power of a tool called “MetaRNN” was useful. Compared with several tools, we confirmed that MetaRNN’s AUC (Area Under the ROC Curve) value was 0.985, which is the best performance. But, it is not enough to judge the pathogenicity of a variant only by the prediction result of the tool. And, prediction tools are also known to be more efficient in predicting missense variants than others. Therefore, it is necessary to examine the pathogenicity of germline variants using both the prediction tool and the clinical significance of ClinVar. In summary, for rare germline variants in cancer studies, it is necessary to observe variants compared to the previous versions of ClinVar. Moreover, if prediction tools are appropriately used, researchers will increase the possibility of finding a variant or gene with more crucial clinical significance to reveal the association between the rare germline variants and cancer development. Citation Format: Seokhyeon Kim, Youngil Koh, Sung-Soo Yoon. Research strategies for rare germline variants and cancer study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2041.
Abstract 2992: Conserved gene fusion ETV6/RUNX1 displays higher immunogenicity than patient-specific missense mutations within the context of HLA-A*02:01
Authors: Erin E. Cygan, Ravi K. Shah, Tanya Kozlik, Paul G. Thomas, Anthony E. Zamora
Journal: Cancer Research (2023)

Abstract Tumor-specific antigens can be targeted by T cells and cancer immunotherapies directed against these neoantigens have resulted in regression across several cancer types. Both missense mutations and gene fusions can serve as targets for cytotoxic T cells, but it is unknown whether one of these classes of mutations has unique parameters that make it more immunogenic. This study compares the immunogenicity of patient-specific missense mutations and a conserved gene fusion, ETV6/RUNX1, present in approximately 25% of pediatric B cell acute lymphoblastic leukemia cases to determine which is more effective at inducing CD8+ T cell responses. Utilizing patient HLA haplotype, mutation data obtained from whole-genome and mRNA sequencing, and the online prediction algorithm NetMHCcons, we identified several putative neoepitopes. To experimentally validate these predicted neoantigens, we performed peptide exchange assays with antigen presenting beads to evaluate the efficiency of peptide-HLA interactions and complex formation. To further investigate the immunogenicity of single nucleotide variants (SNVs) compared to the conserved gene fusion ETV6/RUNX1, we assessed peptide-HLA stability by measuring the dissociation of SNV or ETV6/RUNX1 peptides from the HLA binding groove and calculating the corresponding half-life. Higher affinity peptides would have a greater exchange rate than lower affinity peptides and would have a higher stability/half-life; these assays validated that ETV6/RUNX1 has a greater affinity/stability for HLA-A*02:01 compared to any of the patient-specific SNVs evaluated. To determine whether the higher affinity and stability of the fusion peptide was able to induce greater CD8+ T cell responses, we performed co-culture assays using peptide-pulsed artificial antigen presenting cells expressing HLA-A*02:01 and measured CD8+ T cell cytokine secretion and cytotoxicity. Interestingly, while both mutation types were able to activate CD8+ T cells, those targeting the fusion peptides displayed greater polyfunctionality. Additionally, we found a greater frequency of clonally expanded CD8+ T cells targeting fusion peptides using tetramer-binding assays. Overall, our findings suggest fusion neoantigens have greater immunogenicity than missense mutations and may provide better targets for TCR-T cell-based immunotherapies. Citation Format: Erin E. Cygan, Ravi K. Shah, Tanya Kozlik, Paul G. Thomas, Anthony E. Zamora. Conserved gene fusion ETV6/RUNX1 displays higher immunogenicity than patient-specific missense mutations within the context of HLA-A*02:01 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2992.
Abstract 3035: Phase I trial of alpha-lactalbumin vaccine in high-risk operable triple-negative breast cancer
Authors: George Thomas Budd, Justin M. Johnson, Emily Rhoades, Halle Moore, Holly Levengood, Megan Kruse, Erin Roesch, Jame Abraham, Brenna Elliott, Elena Haury, Rachel Swartz, Holly Pederson, Zahraa Al Hilli, Vincent Tuohy
Journal: Cancer Research (2023)

Abstract Background: Triple-negative breast cancer (TNBC) has a poor prognosis and may be associated with germline mutations. α-lactalbumin (aLA) is expressed in lactating breasts but not at other times or in other tissues. Expression of aLA is found in 70% of TNBC (PMID: 27322324) so could be an immunologic target for TNBC based on the “retired protein hypothesis” (PMID: 31926646). In pre-clinical studies vaccination with aLA inhibited growth of established breast tumors and provided protection from development of autochthonous tumors in transgenic murine models of breast cancer and against 4T1 transplantable breast cancer in BALB/c mice (PMID: 20512124). Methods: To determine the safety and immunogenicity of aLA, patients with early stage TNBC are being entered in a Phase I trial of aLA with GMP-grade zymosan adjuvant in Montanide ISA 51 VG vehicle. Subjects receive 3 vaccinations given once every 2 weeks. Events of Common Terminology Criteria for Adverse Events (CTCAE) grade ≥2 are considered dose-limiting toxicities (DLTs). Results: CTCAE toxicity by dose level is summarized below. All DLTs were injection site reactions, with ulceration and need for incisional drainage representing the grade 3 events. ELISpot assays to determine frequencies of T-cells producing IFN-γ and IL-17 in response to recombinant aLA and ELISA assays of antibody response to aLA will be available in December 2022. Conclusion: Dose level 2 appears to be the maximum tolerated dose. Accrual to dose levels 1 and 2 will be expanded to further define toxicity and immunologic effects. Accrual of patients with BRCA1 or PALB2 mutations planning to undergo prophylactic mastectomy is beginning in order to define the toxicity and immunologic effects in this group and to determine whether inflammatory changes from occult lactational foci will be produced. Funding Source: Department of Defense (W81XWH-17-1-0592 and W81XWH-17-1-0593) Worst Toxicity by Dose Level Dose Level aLAC (mcg) dose Zymosan (mcg) dose n Patients n Grade 0 n Grade 1 n Grade 2 n Grade 3 1 10 10 3 3 2 100 10 3 3 3 500 10 3 2 1 Original 2 100 100 1 1 Citation Format: George Thomas Budd, Justin M. Johnson, Emily Rhoades, Halle Moore, Holly Levengood, Megan Kruse, Erin Roesch, Jame Abraham, Brenna Elliott, Elena Haury, Rachel Swartz, Holly Pederson, Zahraa Al Hilli, Vincent Tuohy. Phase I trial of alpha-lactalbumin vaccine in high-risk operable triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3035.
Abstract 6211: Development and validation of a novel sSTRIDE-MMR functional assay to study the efficiency of MMR inhibitors
Authors: Kamil Solarczyk, Karolina Uznańska, Olga Wójcikowska, Maja Białecka, Agnieszka Waligórska, Szymon Koman, Magdalena Kordon-Kiszala
Journal: Cancer Research (2023)

Abstract Mismatch repair (MMR) is considered to be one of the fundamental pathways that guards genome stability and mutations in genes encoding for crucial MMR proteins have been shown to promote cancer initiation. On the other hand, inactivation of MMR components in cancer cells leads to increased neoantigen formation and in consequence, exposes the tumor to the immune system. Therapeutic strategies aiming at inhibiting MMR are thus under development, yet methods reporting on the status of MMR are lacking. We report here the development, optimization and validation of a first MMR-specific functional assay. The assay, which is based on the STRIDE platform technology, detects DNA nicks localized in close proximity to PMS2 protein and can thus be utilized as a direct reporter of inhibition of PSM2 itself or upstream acting proteins. The optimization phase of assay development was performed in U2OS cells. First, in untreated cells we have shown that the sSTRIDE-MMR signals constitute ca. 10-15% of total single-strand DNA breaks foci detected by the classic sSTRIDE assay variant. In a series of technical negative controls we have then shown that the number of false-positive foci never exceeds 10% of the total number of signals, with as little as 2% for the isotype controls. The assay was further validated in HAP1 wild-type and PMS2-KO isogenic cell line pair. As expected, the number of sSTRIDE-MMR foci in the PMS2-KO cell line was significantly lower than in wild-type cells and additionally, no response to the treatment with 6TG, a known inducer of MMR, was detected in PMS2 null cells. Finally, the assay was used to verify the efficiency of first-in-class small-molecule MMR inhibitors. After treatment with the compounds, the number of detected sSTRIDE-MMR foci was significantly lower when compared to the number of foci in untreated cells. In conclusion, we show here that sSTRIDE-MMR is an assay characterized by high specificity, low false positives rate and a high-dynamic range. We believe that sSTRIDE-MMR can prove to be a very useful cell-based solution to study the efficiency of MMR inhibitors. Citation Format: Kamil Solarczyk, Karolina Uznańska, Olga Wójcikowska, Maja Białecka, Agnieszka Waligórska, Szymon Koman, Magdalena Kordon-Kiszala. Development and validation of a novel sSTRIDE-MMR functional assay to study the efficiency of MMR inhibitors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6211.
Abstract 4942: Heme targeting and its mechanistic role in triple-negative breast cancer suppression
Authors: Eranda Berisha, Maria del Carmen Chacon Castro, Adnin Ashrafi, Narges Salamat, Parinaz Sadat Alemi, Li Zhang
Journal: Cancer Research (2023)

Abstract Breast cancer is the second leading cause of cancer-related deaths and comprises of approximately 30% of all cancer cases affecting women in the United States. There are three subtypes of breast cancer based on receptor profiles, with the third subtype being triple-negative breast cancer. TNBC accounts for about 10-15% of all breast cancers. The TNBC subtype lacks estrogen, progesterone, and HER2 receptors; it is associated with BRCA1 and BRCA2 mutations. This type of cancer has poor prognosis, tends to be more aggressive, and has limited treatment options compared to the other two subtypes. Heme is an essential molecule in the oxidative phosphorylation pathway and in the generation of reactive oxygen species (ROS). ROS generation causes oxidative stress and induces DNA damage in breast cancer. Therefore, targeting its activity potentially suppresses TNBC tumors. Heme-sequestering protein 2 (HeSP2) binds and sequesters heme. It has been shown that HeSP2 treatment of MDA-MB-231 cells inhibited cell proliferation and colony formation. Moreover, HeSP2 suppresses tumor growth in subcutaneously implanted TNBC MDA-MB-231 xenografts in NOD/SCID mice. Furthermore, in vitro studies using murine TNBC cell models 4T1-fluc Neo and EMT6-fluc Puro cells have also shown that cell proliferation and colony formation were inhibited after HeSP2 treatments of increasing concentrations. Thus, these results encourage the potential use of HeSP2 for breast tumor suppression. To further explore the effects of heme targeting and sequestration, we will determine heme flux in TNBC cell models by measuring the levels of heme uptake, export, synthesis, and degradation. Moreover, we will examine mitochondrial markers for OXPHOS complexes in HeSP2 treated TNBC xenografts using immunohistochemical analysis. Further studies are still underway to understand the role of heme in breast cancer, with preliminary results indicating that heme targeting, and sequestration effectively suppress triple-negative breast cancer and its progression. Citation Format: Eranda Berisha, Maria del Carmen Chacon Castro, Adnin Ashrafi, Narges Salamat, Parinaz Sadat Alemi, Li Zhang. Heme targeting and its mechanistic role in triple-negative breast cancer suppression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4942.
Abstract 6191: Temozolomide-associated DNA damage processes related to glioblastoma-immune interactions
Authors: Elizabeth Y. Choe, Forest M. White
Journal: Cancer Research (2023)

Abstract How do cancer cells convert an external perturbation into an interaction with the immune system? The processes associated with antigen presentation remain largely unknown, especially in cancer cells responding to treatment. These intracellular changes may be critical in cancers where immunotherapies need significant optimization, such as glioblastoma. Glioblastoma is also a particularly relevant cancer to characterize the cellular response to perturbations, since all patients currently receive temozolomide, an alkylating agent, regardless of their prognosis. We used mass spectrometry methods to quantify temozolomide-associated changes to the repertoire of peptides presented on MHC class I molecules in vitro over time, as well as the associated changes that occur in DNA damage signaling and protein synthesis. We treated U87-MG cells with temozolomide and directly profiled the peptide-MHC repertoire, ATM/ATR kinase substrate phosphorylation, and newly-synthesized proteins via isotopically labeled and non-canonical amino acid-tagged proteins after 24, 48, and 72 hours. These proteomics approaches identified several MHC-peptides, including phosphorylated peptides, whose presentation changes over time after treatment with temozolomide. We also found that the temporal dynamics of the DNA damage response mirrored that of immunopeptidome remodeling. Additionally, temozolomide alters translation at these time points, with newly-synthesized proteins reflecting internal cell stress processes. These findings suggest potential treatment-associated antigens against which to design vaccines as well as particular signaling nodes that could be modulated with combination therapies to improve presentation of these peptides. Citation Format: Elizabeth Y. Choe, Forest M. White. Temozolomide-associated DNA damage processes related to glioblastoma-immune interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6191.
Abstract 614: CD137 (4-1BB) requires physically associated cIAPs for signal transduction and antitumor effects
Authors: Javier Glez-Vaz, Arantza Azpilikueta, Maria Carmen Ochoa, Irene Olivera, Gabriel Gomis, Asunta Cirella, Carlos Luri-Rey, Maite Álvarez, Sergio Ciordia, Pedro Berraondo, Álvaro Teijeira, Fernando Corrales, Juan M Zapata, Ignacio Melero
Journal: Cancer Research (2023)

Abstract CD137 (4-1BB) is a member of the TNFR family, whose expression is induced on antigen-primed T cells and that mediates potent costimulatory signals upon ligation by CD137L or agonist monoclonal antibodies. CD137 agonists attain immunotherapeutic antitumor effects in cancer mouse models and multiple agents of this kind are undergoing clinical trials. We show that cIAP1 and cIAP2 are physically associated with the CD137 signaling polyprotein complex. Moreover, cIAPs are required for CD137 signaling towards the NF-κB and MAPK pathways and for costimulation of human and mouse T lymphocytes. Functional evidence was substantiated with SMAC-mimetics that trigger proteasomal degradation of cIAPs and transfecting dominant-negative variants of cIAPs. Importantly, antitumor effects of agonist anti-CD137 mAbs are critically dependent on the integrity of cIAPs in cancer mouse models. Citation Format: Javier Glez-Vaz, Arantza Azpilikueta, Maria Carmen Ochoa, Irene Olivera, Gabriel Gomis, Asunta Cirella, Carlos Luri-Rey, Maite Álvarez, Sergio Ciordia, Pedro Berraondo, Álvaro Teijeira, Fernando Corrales, Juan M Zapata, Ignacio Melero. CD137 (4-1BB) requires physically associated cIAPs for signal transduction and antitumor effects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 614.
Abstract 4107: Cytotoxic T cells armed with IL-4 receptor-targeting and PD-L1-blocking peptides inhibits lung tumor growth
Authors: Dong Gyun Jo, Gunassekaran Gowri Rangaswamy, Poongkavithai Vadevoo Sri Murugan, Byungheon Lee
Journal: Cancer Research (2023)

Abstract Tumor homing of adoptively transferred cytotoxic T cells (CTLs) to solid tumors is still inefficient. In addition, CTLs that arrive at tumor tissues meet the immune-suppressive tumor microenvironment. To reduce these limitations in adoptive T-cell therapy against solid tumors, we here exploited CTLs dual-labeled with IL-4 receptor (IL4R)-targeting peptide and programmed cell death-ligand 1 (PD-L1)-blocking peptide. IL4R is commonly upregulated in many solid tumors including lung tumor. PD-L1, an immune checkpoint, is frequently upregulated in tumor cells and contributes to the suppression of CTLs in the tumor microenvironment. CTLs were isolated from the splenocytes of LLC lung tumor-bearing mice and non-genetically labeled with IL4RPep-1, an IL4R-targeting peptide, and PD-L1Pep2, a PD-L1-blocking peptide, using a sulfhydryl-reactive cross linker. Compared to unlabeled CTLs, IL4R-targeted, PD-L1-blocking CTLs showed more robust cytokine secretion and tumor cell lysis during co-culture with LLC tumor cells. The CTLs armed with the dual-acting peptides exerted higher levels of tumor homing and anti-tumor growth activity in LLC lung tumor-bearing mice, which was accompanied by decrease of immune-suppressive cells in the tumor tissues. These results suggest that the IL4R-targeted, PD-L1-blocking CTLs can be a promising strategy in adoptive T-cell therapy against solid tumors. Key words: Adoptive T-cell therapy, CTLs, IL-4 receptor, lung tumor, PD-L1 Citation Format: Dong Gyun Jo, Gunassekaran Gowri Rangaswamy, Poongkavithai Vadevoo Sri Murugan, Byungheon Lee. Cytotoxic T cells armed with IL-4 receptor-targeting and PD-L1-blocking peptides inhibits lung tumor growth. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4107.
Abstract 410: Tumor heterogeneity via AXL activation on primary resistance to EGFR tyrosine kinase inhibitors in EGFR mutated lung cancer
Authors: Tadaaki Yamada, Ryota Nakamura, Hiroyuki Fujii, Takeshi Yaoi, Kyoko Itoh, Shinsaku Tokuda, Koichi Takayama
Journal: Cancer Research (2023)

Abstract Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are the standard treatments for patients with advanced non-small cell lung cancer (NSCLC) harboring EGFR mutations. However, some patients show primary resistance to EGFR-TKIs at the first-line treatment setting. AXL, a member of the TAM family of receptor tyrosine kinase, was reported to be involved in primary resistance to EGFR-TKIs for EGFR mutated NSCLC patients. In the present study, we investigated spatial tumor heterogeneity using autopsy specimens from EGFR mutated NSCLC patients, showing primary resistance to erlotinib plus ramucirumab. qPCR analysis showed that the AXL mRNA expression levels differed in each metastatic site. In addition, the AXL expression levels were likely to negatively correlate with the efficacy of erlotinib plus ramucirumab therapy. The analysis of patient-derived cell lines, established from left pleural effusion before initiation of the treatment, showed that the combination of EGFR-TKIs and an AXL inhibitor remarkably inhibited cell viability compared with EGFR-TKI monotherapy or combination with ramucirumab. Our observations suggested that tumor AXL expression might play a critical role in progression of spatial tumor heterogeneity and primary resistance to EGFR-TKIs for EGFR mutated NSCLC patients. Citation Format: Tadaaki Yamada, Ryota Nakamura, Hiroyuki Fujii, Takeshi Yaoi, Kyoko Itoh, Shinsaku Tokuda, Koichi Takayama. Tumor heterogeneity via AXL activation on primary resistance to EGFR tyrosine kinase inhibitors in EGFR mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 410.